A new beginning from ashes
by comato
Summary: There's been a world war where pokemon trainers fought on the front lines, now pokemon and humans are in constant war. A new generation of pokemon trainers arises, almost by accident, and somehow begins patching things up again. Not my first story, but the first one I've divulging to any kind of public, I'm willing to beg for criticism.
1. Chapter 1

"_We were idiots. We thought our little perfect world was gonna last forever. What nation trains it's children to fight if it does not want war? And when they told us other regions were attacking us, we weren't smart enough to question it. We rushed to "save" our people. At first, there were minor skirmishes. We went in groups, deep into the enemy territory, taking out power plants and similar. And then Kanto and Johto regions formed an alliance."_

"_After that, they didn't stand a chance. After their pokemon were dead, we burned the city down. That's were I lost my Charizard. Two... kids. Defiant, angry kids. Their Solrock and Lunatone teamed up on my Charizard while he was burning the place down. I watched him die. The kids died soon afterwards. The city was burned down to a crisp. We fell back. When reinforcements arrived in the morning, from Lilycove and Sootopolis, there were no survivors left to save."_

"_Soon, all regions were fighting one another. Our experienced pokemon died soon, and there was no time to train the new pokemon. They were sent to us at the front lines, newly captured. Most of my team was alive at that time, so I didn't use the new pokemon. That made me strong. That made me an officer. No one even bothered to catch rare pokemon anymore. Swarms of Butterfree were spraying poison gas at enemy cities, while packs of Bedrill picked of anyone trying to escape."_

"_At one point. We caught too many. There were fewer and fewer pokemon left to capture. So they gave us guns. Told us to fight. And we did. I don't know whose brilliant idea it was to use nuclear weapons, but all the regions got the same idea at once. I used to be called Red. Then they called me Lieutenant- Commander Red, hero of Mossdeep city. Or butcher, depends on the side. And now, they call me the Hermit. I still believe this world can be saved. Even in this dead wasteland there is hope."_

"_Take a look at the world around you. Look, I tell you. Ghost pokemon used to be rare, and look at them now. Pokemon used to stay clear of humans, and now they attack us like rabid dogs. We used to be friends with pokemon. But you wouldn't remember. You've never even seen a pokeball. Well, here... look. This little thing used to contain a pokemon. Only he was never in it. He hated it's guts. How did he get in this? I've got no idea..."_

"_We had scientists back then. And they created all sorts of wonders. Yet, everything they created was used to butcher, to kill. The pokemon in this particular pokeball? Oh, no, he survived the war. He died a few years back. Radiation exposure. He was the last one of my team. He was the first one I got, too. He was sick for years. I traveled the whole world... I hoped a Pokemon center survived somewhere, that I could save him somehow. It was stupid, I know..."_

"_You wouldn't understand it. To you, pokemon are beasts. They are monsters doing their best to end what's left of humanity. But think about it. We did this to them. We forced them to fight and kill each other. We hunted them to use in our war until there were almost none of them left. And then, we dropped down our nukes to kill what little of them remained. When did you last see a Ponyta? A Scyther? Do you even know what a Bulbasaur looked like? I used to have one..."_

"_I don't even find it sad anymore. What happened to us, I mean. We brought it upon ourselves... and pokemon will survive, I hope. I'm only sad that your generation will never know what's it like to be friends with a pokemon. If only your generation could know what pokemon are really like, if only you could stop gunning them down like monsters... No! They are not monsters! They may be broken, savage now, but we made them that way, and we have to fix them."_

"_You don't believe me, don't you? I can't blame you. It's hard to imagine these... pokemon were ever those beautiful, gentle creatures I remember. But they were... and I'm sure they can, again. Here, take this. No, I insist. No! Pikachu is dead, and this pokeball will not bring him back. It might be the last one in the world, I don't know. Take it. Go out there and capture a pokemon. Why? I don't know. Maybe I hope you will change the world back. I've lost everything. Don't take my dreams away."_

Sam could remember that speech clear as day, he'd taken the red and white ball with a sense of reverence and dread, not knowing how to tell him that it was the stupidest idea ever conceived, but honoured that he would give him his most treasured possession nevertheless; afterwards for a time Red, or Ash like Sam was allowed to call him, seemed more at peace, more...relaxed, until in one of those skirmishes he had to participate every now and again he got the perfect chance to save a rare caterpie, no one would have to know, it was small enough that he could've hidden it somewhere, nurtured it to health, all of this still in time for Red to see the beginnings of that hope he had so desperately craved for, instead he shot it down in cold blood.

Red never found out, not technically, but Sam never had much guts in the first place, for anything; as his guilt grew and his visits to his only friend, parent, and brother became a rarer occurrence he became certain that Red had guessed. Red died a year later, and it had been months since his last visit whereas before they all but lived together, nobody had even found out, not until Sam came over and noticed the stink, he'd been decomposing for days. That night he locked himself in a bathroom, sobbed for hours on end cradling the stupid ball to his chest, missed the funeral and all, apparently General Gary had asked for him, wondering why he hadn't shown up, why he was the only one there, of course he didn't want to be, whatever else Red might've degraded to in his last few years he had also been The War Hero and the general had to make an example of honouring their veterans, not that it made the ordeal any more pleasant.

It had already been a couple of months since then, and Sam had never been more miserable, he had never been very good at making friends, or getting along for that matter, and guilt and misery for a man everybody else had thought was a crack pot with schizophrenia didn't help, his interaction with other was limited to what was absolutely necessary so that sometimes he'd go days without uttering a word. Today he was on patrol duty in a team of six, he put on his vest, made sure that he had ammunition and emergency pills, loaded a plasma machine gun, standard now with so many ghost pokemon. While he was doing all this their captain was giving them the usual speech about their duties, and what exactly it was that they were supposed to do today, as if they didn't know it by heart already, once that was finally over they got on the pickup truck and drove fifteen miles east, where they would relieve another team of duty, camp for a month under the stars, then whatever came next.

An uneventful trip, where, as ever, Sam talked to no one and no one talked to Sam. The rest of their assignment proceeded in a similarly predictable fashion, until in one of the many times they had to go out and see what their traps had yielded, and reinstate the ones that had sprung, he found a Fortare, a ghost-fighting type, not exactly uncommon, but they rarely ventured so near until they had evolved. This one was dead by the looks of it, gently so as to not touch the electrical wiring he removed what he believed was decomposing smoke, until it opened a bleary eye and looked at him, in about as much shock as Sam must've been feeling at that moment. Not actually knowing what he was doing he finished leaving the pokemon on the ground right besides him and, as he caressed its head with one hand finished with the wiring trap with one hand, and only then did he steal a good look at the pokemon.

It was mostly a blob of smoke, only its face and hands being truly recognizable, both fists were easily as big as the rest of his body, and his face was half buried in the ground, while it spied him with a single eye, as if it were shy. Too afraid of going for his gun he instead left a rations pill for him to eat, and when it finally turned to look at the white thingy he then made a break for it. He checked two more traps before reuniting with the rest of the team at camp, where he settled at the very edge of the camp behind a tent to read, the pokemon was there, peeking from behind a tree, floating in a lopsided manner, nibbling on the pill he'd given it. The moment he caught sight of it scuttled behind a tree and tried peeking at him from the other side of the same tree, Sam couldn't help but smile, but confused all the same, almost by accident he started to caress the pokeball, funnily enough he didn't actually know how capturing it was supposed to be done, but he had a feeling that it wouldn't be too difficult.

Instead he took out another pill and offered it to the pokemon, who hesitantly at a baby's pace, started gliding towards him, before rushing the final distance and scooping up the little pill settling to cuddle by his leg. It seemed quite content to take its time with it, admiring every bite for a while as it juggled it between its giant fists, tentatively Sam tried caressing it like he did before, it didn't seem to mind, or notice for that matter. A snapped twig made Sam turn his head, and look up to see John aiming at the little critter with his plasma shotgun but looking at him at a complete loss as to what to do next, he shook his head, and what followed was a series of hesitant jerky movements on John's part: he started to point his gun upwards, seemed to think better of it and stopped, leaving his gun pointing at some random direction right over Sam's head, next he tried retreating only to find that he was stepping on a particularly crunchy leaf and stopped there balancing on the balls of his feet.

"what are you doing?" this was said by captain who had walked up behind John with his gun at the ready, only to stop just as dead in his tracks when he saw the commotion; all the while the little Fortare remained oblivious to the potential danger, instead it had taken the liberty of climbing up Sam's vest in search of some other edible snack, revealing in the process, for the first time in their recorded history, that it's fists could actually unclench into four puzzle like fingers.

"should we shoot it?" John asked.

"we'll hit Sam too."

"how did this even happen?"

"it was in the wiring traps."

"...and."

"i thought it was dead, only it wasn't, I couldn't go for the gun so instead I gave it a snack."

"so he likes pills?"

"now what?" John asked captain.

"i don't know, can you get rid of it?"

"if it only stays for the pills it's bound to leave eventually if we stop feeding it."

"no dinner for you tonight then." and with that he motioned the rest to leave and Sam was left to wait till the little critter got bored and left, only, that never happened, it did leave his side a couple of time, but no more than a few paces when it, somehow, despite it's inconsistency, rolled off of him while it was playing with his now, mostly empty pockets, then when it was finally starting to get tired the little bastard had the gal to cuddle itself in the crook of his neck and fall asleep there. That's how the captain found him in the morning, Sam still sitting against the pole of the tent, his head bent forwards in an uncomfortable position and the Fortare hanging by his neck, both still completely asleep.

that's the first entry, for starters I need to point out that everthing that's written in cursive was actually written by a guy in 9gag in the comments section:  
>gag/aDwgEEN

and that the whole inspiration for the idea came entirely from that, unfortunately he didn't seem too thrilled at writting fan fiction, so I took the liberty of having a stab at it myself.

Secondly that as far as I got stuck, and because it's been a week and I haven't unstuck, I'm gonna take the lazy way out and continue after a time jump, (short one)


	2. Chapter 2

The following week was a period of his life Sam had mixed feelings about that he would never come to terms with, in the hope of driving the pokemon away they started excluding them both, but never quite daring to actually drive away the Fortare; what little human contact he was used to vanished, and in addition, due to it's stupid habit of eating the food that was meant for him, they had started to starve them both out, only the pokemon had the ability of sneaking off for food when nobody was paying attention (sometimes from camp), and more less feed them both, which Sara and John both found adorable. It was around this time that they gave up hope on the critter of ever leaving and instead welcomed them both back in and decided that they'd figure out what to do before they had to go back. Somehow, through unspoken consent, or fear of being the only one against five, no one mentioned the possibility of gunning the pokemon despite the number of opportunities.

"I suppose you could turn into a runner." John proposed cheerfully, of the six of them the pokemon only trusted Sam, he was the only one he'd sleep with at night, and the only one who's hand he would eat of, but John had taken a much greater liking to it and he was second for the pokemon's affection. It was a good idea really, flying pokemon had made it impossible to set up radio communications over long distances because of how they kept knocking the antenna out, so instead traditional messengers were used, they spent the great vast majority of their time out in the wilderness, the privacy was perfect for whatever it was he decided to do with the pokemon, except they always traveled in pairs, and it was one of the highest paying jobs due to the dangers.

"i'd need a partner."

"i wouldn't mind, heck, maybe i'll look for a pet of my own." that made Sara, the only girl in the group, to turn her head, the rest pretended not to have heard that. "by the way, are you gonna give it a name?"

"i don't actually intend to keep it."

"'course you are, otherwise you would've shot it by now."

"neither of you can become runners off the bat, you have to meet certain standards." the captain interrupted.

"like...?"

"for starters neither of you are a good enough shot, neither of you can cook, neither of you have ever been outside our quarantined area, and your hunting skills are mediocre at best."

"i thought runners were given supplies?"

"only enough to make it to the destination under idealized circumstances, and something always happens, you're bound to run into other not so friendly pokemon along the way." Sam gave it a long hard stare, Sara liked to keep her distance, had refused to part with her gun and had gone from fairly chatty to being quiet and looking over her shoulder every minute, the rest were gradually calming down, except for John, who made it look as if he'd grown up under these circumstances. He did like to muse over the idea of killing it off, somehow he just couldn't manage to get up and do it, always a reason, it wouldn't be difficult, it didn't even find it bothering when Sam went for his gun, plasma or physical, as a result his excuses of late had been laziness, whereas before he'd never been lazy, simply unwilling.

"i think I could make it, I was pretty good at controlling C-weapons back at BC."

"were you really?" Sara asked in surprise. C-weapons meant Corpse Weapons, they didn't always refer to weapons strictly speaking, some really high quality materials from dead pokemon were used, good armoured quads were made from Aggron skin, and these were also referred as such despite no intended offensive use, but then there was the sixteen double cannons that surrounded their HQ, which had been taken, as they were, from dead Blastoise, or the slightly more mobile weapons, like the vambraces of Mega Blastoise or "dead" Honedge's.

"that's an advantage, but it doesn't guarantee you a spot."

"they're always short on runners, why wouldn't they take us Cap?"

"are you two really going to do that?" Sara asked.

"'course he is, if he was gonna shoot it he would've done it by now, besides he doesn't like people anyway, he was born to be a runner."

"he still needs to pass a test."

"is it difficult?"

"yes, you have to make it to another HQ to deliver a message."

"so the test is to actually do the job?"

"they give you an escort of sorts, another proper runner team doing the real delivery, as far as both groups are concerned the other doesn't exist, but if the newbies get in trouble, and it's possible for the runners to save them, they have to give it a try, then you fail of course."

"can you just request for the test? It really doesn't sound that difficult."

"the minimum distance you'd have to cross is seven kilometres, if you can manage to make a straight line, which you won't, through territory where pokemon live."

"how do they normally manage?" Sam asked.

"they know the land, depending on the landscape they can figure out what kind of pokemon live there, and how to avoid them, there's a forested area nearby for example, that's crawling with flying types, you can only move at night, when they're sleeping, but you have to do that near the treetops to avoid the nocturnal pokemon that come out at night at ground level, and you have to do that without disturbing their sleep either."

"what happens if you try to go around?"

"sometimes your food doesn't last in a place you can't hunt, sometimes you have a letter that can't wait that long, other times there's a nest that's blocking your exit and you can't take your favourite route."

"did you work as a runner?"

"my brother did, I didn't see much of him, he never returned from his last assignment. The pay was great though, whenever he was around he always had plenty to invite drinks for at least a round."

"that's nice, what kind of special weaponry do they give you?" John asked.

"depends, actually they get their pick, as long they have in stock."

"i think we should give it a try, c'mon mate, maybe even Luggy'll help us out, like pokemon did in all the stories your friend told."

"do you two seriously believe all of this crap?" Sara exploded.

"Luggy's been with us for two weeks, and look at him, he's almost like a toddler." John answered, an arguable statement, the pokemon had run to Sam at her outburst, but rather than hiding behind he was standing in front of him protectively and threateningly.

"and why is he Luggy?"

"Sam wasn't naming him, no one told me I couldn't do it." he answered with a shrug.

"i don't wanna kill it." Sam interrupted, John grinned at him.

"i didn't wanna learn how to use a gun when I was kid, doesn't mean that I didn't have to."

"he hasn't hurt you."

"i've never been hurt by most of the pokemon that exist, doesn't mean that i'd stick around if offered the company." John was about to retort in Sam's stead when their alarm went off, the argument was dropped in a heart beat, as everybody went for their guns, for the first time since Luggy had joined them he was confused and scared. Sam in an attempt to keep the critter under control grabbed it by it's hands and forced it to keep close as he hid behind their somewhat crude line of defence. The alarm was only supposed to go off it a certain number of pokemon crossed a barrier they had set up some distance away, otherwise they relied on their traps to stop the few wanderers, or a lookout if one of the strays got through.

Pokemon cries could be heard from the distance as they feel into the traps, but the cries were getting steadily louder. Lugg was visibly torn, Sam hugged him a little tighter as he wondered if it wouldn't punch his ribs in while the fight was going on, nothing he could do at this point, nothing good would happen if he tried to shoot it now with tensions as they were, except maybe try to keep it from getting a good look at things.

"Sam? What's Luggy doing?" the captain asked, Sara started muttering under he breath.

"he's fine, nervous but i'm cuddling him up, he won't do anything." the pokemon were only moments away from crashing within line of sight, behind them the beeper gave two green flashes, it meant that at least two pokemon on their third evolution had survived the kill zone.

"ima' kill ya later Sam." Sara said, just as they came through. The two tanks they'd been warned about were the first to distinguish themselves, followed by a ragtag group of twenty, already injured, weaker pokemon.

"Sara, poison." she took her gun and shot at a marker they had further out, the gas poison exploded in a giant cloud engulfing the whole host, and making Luggy squirm in his grip. The tactic did little to help, one of the weaker pokemon fell dead in his tracks, but the rest continued unbothered.

"Fire at will!" and they did, the sound made Luggy stop squirming and instead started hugging so tightly it hurt. They focused mostly on the two stronger ones, their attacks were the strongest, and more importantly had longer range, for one of them 20 metres was more than enough, and his fist came flying at them, smashed through their barricade hitting both Sara and John squarely, both were sent flying backwards, at least one of them wouldn't be moving for a while, but neither of them should've died from that.

At this time the pokemon were running into their last line of defences, they activated a firewall frying a dozen of the smaller ones, but doing little damage to the Fist Flyer. Out of the haze a dart came and struck Shaun squarely in the chest, probably a Velonorm, but hard to say, he needed antidote now though, the captain was the nearest one, and it fell to him to drop his gun and inject him with antidote. Captain wouldn't be back to shooting for a few minutes, Shaun was out of commission and out of Sara and John only Sara was coming back around; Sam shifted his aim towards the feet and legs of the larger pokemon, the traps they had left could probably take care of the smaller ones, but the larger ones needed to be slowed, somewhere to his right Jonah did the same.

They were making good progress as the pokemon either fell back or died due to electrocution, dismemberment and other causes until Lugg let go suddenly, did something Sam didn't quite catch and the entirety of his vision more than a meter away turned into a solid wall of smoke, literally held at bay as if by a wall; not knowing was else to do Sam hugged Lugg to him to keep him from doing anything else, to his right Jonah kept firing, and behind him captain left Shaun and ran somewhere to the left, a few minutes went by, during which Sam had to move for lack of visibility and finally an incredibly annoying sound in the distance, captain must've activated their sonographm, it would confuse anyone that stood within an area of effect, though it would possibly not do any good at this point, it looked like they'd won, if only barely.

The whole fight had barely lasted more than thirty minutes, but Shaun was still comatose, Sara was having trouble coming around, John had a huge bump in his head and wasn't waking up; out of the six, only half were entirely alright, and Lugg was trying to take a walk among the remains of the battlefield. Sam wouldn't let him, he kept a firm grip on one of his fists while Lugg struggled, oddly weakly, as if it were sick. Jonah was operating a thermal camera on the surroundings, trying to see if there was anything left, and he took fifteen minutes to confirm that it was safe, only then, and reluctantly at that, did Sam allow Lugg to leave as he tried taking a closer look at John's head.

"Sam, your pet." Jonah said as he was keeping a lookout.

"What's he doing?"

"walking around, not really doing anything. He stopped to look at one of the corpses, the opulenter." he didn't know what that might mean, he knew perfectly well what an opulenter was, the final evolution of a fortare, he should've realized what it was when those two smoke punches came flying at them.

"let me know if he does anything."

"he protected you, didn't he?"

"he did what?" the captain asked suddenly.

"the second time the opulenter threw a punch Lugg cast Protect." Jonah asked.

"is that true?"

"i think it must be, one moment I was shooting, the next my line of sight was completely blocked by loads of smoke, it did feel like there was a wall there though."

"i was watching from the sidelines, Lugg cast protect, I saw the blue shimmer." Jonah volunteered.

"did he do anything else?"

"no." Sam answered.

"i didn't see anything."

"where is he now?"

"looking at the corpses."

"keep a gun ready, just in case."

Sara really was having a hard time getting around, even though she had woken up almost immediately, John almost certainly had a broken jaw and maybe a cracked skull, and Shaun had a puncture wound. What exactly had happened shouldn't have happened, like all civilians they were trained at arms, and were required to spend a few hours a week protecting the border, pokemon weren't smart, they attacked any human that was within reach, completely ignoring the concept of tactics, it allowed them to make a defence which in theory would be laughable, but even so, such a force shouldn't have penetrated so far past the initial defences.

Captain called in to report immediately and requested back up, or at least a medical team, while Sam and Jonah were sent to reinstall the most important of the traps, and the scouting units. That afternoon captain called in Sam for a private word after he announced that said reinforcements would be there by tonight.

"congratulations on getting a pokemon to actually help you."

"thank you sir."

"due to reasons the whole of our team is being pulled back to HQ, your pet is still with you, you gonna shoot it or not?"

"are you gonna let me not to?"

"if you have a plan." Sam didn't have a plan, on the other hand he knew for certain that he didn't want to part ways with Lugg, he wasn't sure if he actually liked the pokemon, if he was just attached, or if it was simply the only creature that approached him out of its own volition and he happened to be lonely.

"take it back to HQ, i'll be a runner."

"and once you're there?"

"you've read my file, you know what my lifestyle is like, I can keep Lugg hidden."

"and how do you intend to get there without drawing attention?"

"i have a pokeball." he said as he showed him.

"where did you get that?" he asked; pokeballs, as items solely designed for carrying pokemon as weapons, a concept that was considered worse that nuclear strikes, had all been supposedly destroyed through unspoken consensus.

"my crackpot friend had it, it belonged to his best friend."

"...why should I let you do this?"

"why didn't you do anything about it before?"

his captain didn't answer, instead he just stared at him. "fine, have a go at it, but you need a partner, runners don't run alone, you'll have to ask John, and that's a big favor you're asking." Sam left the tent to rummage in his bags looking for the pokeball, while Luggy trailed behind him, the bag was where he left it, buried at the very bottom of his bag, only then did he realize he had absolutely no idea how this thing worked, the only indication was the button in the middle, but the moment he pressed it the whole thing dissembled into two half spheres, and a dozen different sized rings; the first thing that Sam wondered is what Red's reaction would've been, or his advice, he'd mentioned that his best friend had hated the ball, _good riddance_ he thought dully.

**i want to, again, stress my need for criticism, please, and would also ask, of all the companions Ash has had in the anime, who's a favorite? i wanna write one in as a cameo, of sorts...not sure what role they'll be playing yet.**

**also, in case it isn't obvious yet, i'm not very good with inventing pokemon names, i'm open to suggestions, and yes i'm introducing mostly new ones because, as stated in the intro, most are now pokemon**


End file.
